|
| Status |
Public on Oct 31, 2014 |
| Title |
Blood_Test3_1 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood_IS900-PCR positive
|
| Organism |
Bos taurus |
| Characteristics |
gender: female
sample group: IS900-PCR positive, MAP-ELISA positive
tissue: Peripheral Blood
|
| Treatment protocol |
The cattles were evaluated for disease status by a commercial ELISA (IDEXX Laboratories, Inc., Westbrook, ME, USA) for the detection of MAP-specific antibodies and for IS900 and ISMap02 by fecal PCR. Blood samples from the cattle were immediately collected into PAXGene Blood RNA tubes (PreAnalytiX/Qiagen, Hilden, Germany).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated from blood of the cattle according to the manufacturer's instructions using a PAXGene blood RNA kit (PreAnalytiX/Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA was prepared from 5 μg total RNA according to the manufacturer’s instructions using the Agilent’s Quick Amp Labeling Kit (Agilent Technologies, Inc.).
|
| |
|
| Hybridization protocol |
Following fragmentation, 1.65 μg of labeled cRNA was hybridized to the Agilent expression microarray according to the protocols provided by manufacturer.
|
| Scan protocol |
The arrays were scanned using the Agilent Technologies G2600D SG12494263 (Agilent Technologies, Inc.).
|
| Description |
Test3 001
|
| Data processing |
Array data export processing and analyses were performed using Agilent Feature Extraction v11.0.1.1 (Agilent Technologies, Inc.).
Array probes were filtered by p < 0.05 (similar to the signal to noise ratio) in at least 50% of samples. Array probes were transformed by logarithm and normalized by quantile method. Statistical significance of the expression data was determined using the local pooled error (LPE) test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.
|
| |
|
| Submission date |
Oct 30, 2014 |
| Last update date |
Oct 31, 2014 |
| Contact name |
Min-Kyoung Shin |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University
|
| Street address |
1, Gwanak ro, Gwanak gu
|
| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11649 |
| Series (1) |
| GSE62835 |
Transcriptional profiling of whole-blood in Mycobacterium avium subsp. paratuberculosis-infected cattle |
|
